The structure of the left‐handed antiparallel amylose double helix: Theoretical studies

<jats:title>Abstract</jats:title><jats:p>The atomic coordinates from the crystal structure of a hexasaccharide complex accommodating a zigzag polyiodide [ W. Hinrichs, G. Büttner, M. Steifa, Ch. Betzel, V. Zabel, B. Pfannemüller, and W. Saenger (1987) <jats:italic>Science</jats:italic> Vol. 238, pp. 205–208; W. Hinrichs and W. Saenger (1990) <jats:italic>Journal of the American Chemical Society</jats:italic>, Vol. 112, pp. 2789–2796 ] served to construct an antiparallel‐stranded amylose double helix with a 5 Å wide central cavity. Using our methodology for the energetic optimization of polymer structures in the internal/ helical variable space [ H. Sklenar, R. Lavery, and B. Pullman (1986) <jats:italic>Journal of Biomolecular Structure Dynamics</jats:italic>, Vol. 3, pp. 967–987, 989–1014; 1015–1031], we have calculated a theoretical counterpart of this idealized double helix by constraining the helical twist and rise to their experimental values (−45° and 2.33 Å, respectively). Applying the same constraints to the parallel‐stranded duplex, this also leads to a low‐energy structure with wide central cavity. It is considered as an alternative model to accommodate iodine as observed in the starch–iodine complex.</jats:p><jats:p>Release of the helical constraints leads to left‐handed antiparallel‐ and parallel‐stranded double helices, respectively, with narrow central cavities. Both structures have very similar helix parameters and correspond, in their main characteristics, to the experimentally derived parallel‐stranded structure of amylose in starch (6 residues per turn and a pitch height of about 21 Å). The intramolecular energy calculated for the optimized antiparallel‐stranded amylose double helix is comparable to that of the parallel‐stranded structure. This result raises the question why parallel‐stranded amylose seems to be favored in nature. © 1993 John Wiley & Sons, Inc.</jats:p>